[MINC-users] minc file is not visible in register but is visible in Display
Vladimir S. FONOV
vladimir.fonov at gmail.com
Thu May 18 16:02:39 EDT 2017
It's a bug in certain versions of register, affecting it's ability to
show files stored in float, with low values.
Can be fixed by mincreshape -short
On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote:
> Hi,
> I have a file that when viewed in register is not viewable at all. It is
> just blank (black) everywhere no matter what I do with the windowing.
> When I load it in Display it is just fine, so I know the data is there.
>
> It is a systemic problem, i.e., all files that are created with my script
> have this problem of not being visible in register.
>
> I'm wondering if it has something to do with the range of my data because
> if I do further operations on it, then the downstream files load okay.
>
> For example, the file that currently does not load is subject_t2map.mnc.gz
> which contains float values from 0 to 1.
>
> If I do something like this, then the resulting 100.mnc loads just fine in
> register:
> minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc
>
> Here are the mincstats of my file with/without a mask:
>
> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz
> File: subject_t2map.mnc.gz
> Mask file: (null)
> Total voxels: 3932160
> # voxels: 2178980
> % of total: 55.41432699
> Volume (mm3): 6536940
> Min: 0
> Max: 0.9998887777
> Sum: 415156.0653
> Sum^2: 161711.3365
> Mean: 0.1905277081
> Variance: 0.03791344611
> Stddev: 0.1947137543
> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075
> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081
>
> Histogram: (null)
> Total voxels: 3932160
> # voxels: 2178980
> % of total: 55.41432699
> Median: 0.1142372932
> Majority: 0.0002499721886
> BiModalT: 0.3392122686
> PctT [ 0%]: 0.0002499721886
> Entropy : 9.187178001
>
> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask
> subject_t2map_mask.mnc.gz -mask_binvalue 1.0
> File: subject_t2map.mnc.gz
> Mask file: subject_t2map_mask.mnc.gz
> Total voxels: 3932160
> # voxels: 1962553
> % of total: 49.91030375
> Volume (mm3): 5887659
> Min: 0.01020694431
> Max: 0.9998887777
> Sum: 415156.0653
> Sum^2: 161711.3365
> Mean: 0.211538779
> Variance: 0.0376498199
> Stddev: 0.194035615
> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075
> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081
>
> Histogram: (null)
> Total voxels: 3932160
> # voxels: 1962553
> % of total: 49.91030375
> Median: 0.1242361822
> Majority: 0.09273968637
> BiModalT: 0.3552104831
> PctT [ 0%]: 0.0002499721886
> Entropy : 9.681988728
>
>
> And here is the full mincheader:
> localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz
> netcdf mincheader-18621-tmp {
> dimensions:
> zspace = 60 ;
> yspace = 256 ;
> xspace = 256 ;
> variables:
> double zspace(zspace) ;
> zspace:varid = "MINC standard variable" ;
> zspace:vartype = "dimension____" ;
> zspace:version = "MINC Version 1.0" ;
> zspace:comments = "Z increases from patient inferior to superior" ;
> zspace:spacing = "regular__" ;
> zspace:alignment = "centre" ;
> zspace:step = 3. ;
> zspace:start = -53.5106888535874 ;
> zspace:spacetype = "native____" ;
> zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855,
> 0.997490804617524 ;
> int yspace ;
> yspace:varid = "MINC standard variable" ;
> yspace:vartype = "dimension____" ;
> yspace:version = "MINC Version 1.0" ;
> yspace:comments = "Y increases from patient posterior to anterior" ;
> yspace:spacing = "regular__" ;
> yspace:alignment = "centre" ;
> yspace:step = -1. ;
> yspace:start = 201.955416409066 ;
> yspace:spacetype = "native____" ;
> yspace:direction_cosines = 0.0303997023189596, 0.997088076060185,
> 0.0699373053349794 ;
> int xspace ;
> xspace:varid = "MINC standard variable" ;
> xspace:vartype = "dimension____" ;
> xspace:version = "MINC Version 1.0" ;
> xspace:comments = "X increases from patient left to right" ;
> xspace:spacing = "regular__" ;
> xspace:alignment = "centre" ;
> xspace:step = -1. ;
> xspace:start = 128.433460913677 ;
> xspace:spacetype = "native____" ;
> xspace:direction_cosines = 0.999498332440992, -0.0297021098791549,
> -0.0109940036566919 ;
> double image-max(zspace) ;
> image-max:varid = "MINC standard variable" ;
> image-max:vartype = "var_attribute" ;
> image-max:version = "MINC Version 1.0" ;
> image-max:_FillValue = 1. ;
> image-max:parent = "image" ;
> double image-min(zspace) ;
> image-min:varid = "MINC standard variable" ;
> image-min:vartype = "var_attribute" ;
> image-min:version = "MINC Version 1.0" ;
> image-min:_FillValue = 0. ;
> image-min:parent = "image" ;
> float image(zspace, yspace, xspace) ;
> image:parent = "rootvariable" ;
> image:varid = "MINC standard variable" ;
> image:vartype = "group________" ;
> image:version = "MINC Version 1.0" ;
> image:image-max = "--->image-max" ;
> image:image-min = "--->image-min" ;
> image:valid_range = 0.f, 0.9998888f ;
> image:complete = "true_" ;
> int rootvariable ;
> rootvariable:varid = "MINC standard variable" ;
> rootvariable:vartype = "group________" ;
> rootvariable:version = "MINC Version 1.0" ;
> rootvariable:parent = "" ;
> rootvariable:children = "image" ;
>
> // global attributes:
> :ident = "redacted" ;
> :minc_version = "2.2.00" ;
> :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult
> subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n",
> "" ;
> }
>
>
> And here is my minc package info stuff:
> localhost[~/nrx/t2map]$ which register
> /opt/minc-toolkit/0.3.16/bin/register
>
> localhost[~/nrx/t2map]$ register -version
> register: Version: 1.4.00
>
> localhost[~/nrx/t2map]$ mincstats -version
> program: 2.2.00
> libminc: 2.2.00
> netcdf : 4.2.1 of Feb 19 2015 15:50:30 $
> HDF5 : 1.8.8
>
> localhost[~/nrx/t2map]$ cat /etc/system-release
> CentOS release 6.5 (Final)
>
> localhost[~/nrx/t2map]$ uname -a
> Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19
> 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>
> Any come across this bug before? Any ideas on how to fix it so it is
> viewable in register?
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
--
Best regards,
Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
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